niman Posted March 24, 2016 Report Share Posted March 24, 2016 (edited) Fundacao Oswaldo Cruz has release a full Zika sequence, Rio-U1, from urine collected from a Rio de Janeiro patient on Jan 14,2016 http://www.ncbi.nlm.nih.gov/nuccore/KU926309 Edited March 24, 2016 by niman Link to comment Share on other sites More sharing options...
niman Posted March 24, 2016 Author Report Share Posted March 24, 2016 LOCUS KU926309 10795 bp ss-RNA linear VRL 21-MAR-2016 DEFINITION Zika virus isolate Rio-U1, complete genome. ACCESSION KU926309 VERSION KU926309.1 GI:1006593051 KEYWORDS . SOURCE Zika virus ORGANISM Zika virus Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; Flavivirus. REFERENCE 1 (bases 1 to 10795) AUTHORS Bonaldo,M.C., Ribeiro,I.P., Lima,N.S., Santos,A.A.C., Raphael,L.M.S., Cruz,S.O.D., Mello,I.S., Furtado,N.D., Moura,E.E., Castro,M.G., Gerber,A.L., Almeida,L.G.P., Lourenco-de-Oliveira,R., Vasconcelos,A.T.R. and Brasil,P. TITLE Isolation of infective Zika virus from urine and saliva of patients in Brazil JOURNAL Unpublished REFERENCE 2 (bases 1 to 10795) AUTHORS Bonaldo,M.C., Ribeiro,I.P., Lima,N.S., Santos,A.A.C., Raphael,L.M.S., Cruz,S.O.D., Mello,I.S., Furtado,N.D., Moura,E.E., Castro,M.G., Gerber,A.L., Almeida,L.G.P., Lourenco-de-Oliveira,R., Vasconcelos,A.T.R. and Brasil,P. TITLE Direct Submission JOURNAL Submitted (16-MAR-2016) Laboratorio Nacional de Bioinformatica / Laboratorio Nacional de Computacao Cientifica, Laboratorio de Biologia Molecular de Flavivirus / Fundacao Oswaldo Cruz, Rua Getulio Vargas, 333, Petropolis, RJ 25651075, Brazil COMMENT ##Assembly-Data-START## Assembly Method :: Ray v. 2.2 Coverage :: 8000 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..10795 /organism="Zika virus" /mol_type="genomic RNA" /isolate="Rio-U1" /isolation_source="urine" /host="Homo sapiens" /db_xref="taxon:64320" /country="Brazil" /collection_date="14-Jan-2016" /note="passage details: Vero cells" 5'UTR 1..100 CDS 101..10372 /codon_start=1 /product="polyprotein" /protein_id="AMQ48981.1" /db_xref="GI:1006593052" /translation="MKNPKKKSGGFRIVNMLKRGVARVSPFGGLKRLPAGLLLGHGPI RMVLAILAFLRFTAIKPSLGLINRWGSVGKKEAMEIIKKFKKDLAAMLRIINARKEKK RRGADTSVGIVGLLLTTAMAAEVTRRGSAYYMYLDRNDAGEAISFPTTLGMNKCYIQI MDLGHMCDATMSYECPMLDEGVEPDDVDCWCNTTSTWVVYGTCHHKKGEARRSRRAVT LPSHSTRKLQTRSQTWLESREYTKHLIRVENWIFRNPGFALAAAAIAWLLGSSTSQKV IYLVMILLIAPAYSIRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIE LVTTTVSNMAEVRSYCYEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWG NGCGLFGKGSLVTCAKFACSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHET DENRAKVEITPNSPRAEATLGGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWF HDIPLPWHAGADTGTPHWNNKEALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAE MDGAKGRLSSGHLKCRLKMDKLRLKGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAG TDGPCKVPAQMAVDMQTLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVG EKKITHHWHRSGSTIGKAFEATVRGAKRMAVLGDTAWDFGSVGGALNSLGKGIHQIFG AAFKSLFGGMSWFSQILIGTLLMWLGLNTKNGSISLMCLALGGVLIFLSTAVSADVGC SVDFSKKETRCGTGVFVYNDVEAWRDRYKYHPDSPRRLAAAVKQAWEDGICGISSVSR MENIMWRSVEGELNAILEENGVQLTVVVGSVKNPMWRGPQRLPVPVNELPHGWKAWGK SYFVRAAKTNNSFVVDGDTLKECPLKHRAWNSFLVEDHGFGVFHTSVWLKVREDYSLE CDPAVIGTAVKGKEAVHSDLGYWIESEKNDTWRLKRAHLIEMKTCEWPKSHTLWTDGI EESDLIIPKSLAGPLSHHNTREGYRTQMKGPWHSEELEIRFEECPGTKVHVEETCGTR GPSLRSTTASGRVIEEWCCRECTMPPLSFRAKDGCWYGMEIRPRKEPESNLVRSMVTA GSTDHMDHFSLGVLVILLMVQEGLKKRMTTKIIISTSMAVLVAMILGGFSMSDLAKLA ILMGATFAEMNTGGDVAHLALIAAFKVRPALLVSFIFRANWTPRESMLLALASCLLQT AISALEGDLMVLINGFALAWLAIRAMVVPRTDNITLAILAALTPLARGTLLVAWRAGL ATCGGFMLLSLKGKGSVKKNLPFVMALGLTAVRLVDPINVVGLLLLTRSGKRSWPPSE VLTAVGLICALAGGFAKADIEMAGPIAAVGLLIVSYVVSGKSVDMYIERAGDITWEKD AEVTGNSPRLDVALDESGDFSLVEDDGPPMREIILKVVLMTICGMNPIAIPFAAGAWY VYVKTGKRSGALWDVPAPKEVKKGETTDGVYRVMTRRLLGSTQVGVGVMQEGVFHTMW HVTKGSALRSGEGRLDPYWGDVKQDLVSYCGPWKLDAAWDGHSEVQLLAVPPGERARN IQTLPGIFKTKDGDIGAVALDYPAGTSGSPILDKCGRVIGLYGNGVVIKNGSYVSAIT QGRREEETPVECFEPSMLKKKQLTVLDLHPGAGKTRRVLPEIVREAIKTRLRTVILAP TRVVAAEMEEALRGLPVRYMTTAVNVTHSGTEIVDLMCHATFTSRLLQPIRVPNYNLY IMDEAHFTDPSSIAARGYISTRVEMGEAAAIFMTATPPGTRDAFPDSNSPIMDTEVEV PERAWSSGFDWVTDHSGKTVWFVPSVRNGNEIAACLTKAGKRVIQLSRKTFETEFQKT KHQEWDFVVTTDISEMGANFKADRVIDSRRCLKPVILDGERVILAGPMPVTHASAAQR RGRIGRNPNKPGDEYLYGGGCAETDEDHAHWLEARMLLDNIYLQDGLIASLYRPEADK VAAIEGEFKLRTEQRKTFVELMRRGDLPVWLAYQVASAGITYTDRRWCFDGTTNNTIM EDSVPAEVWTRHGEKRVLKPRWMDARVCSDHAALKSFKEFAAGKRGAAFGVMEALGTL PGHMTERFQEAIDNLAVLMRAETGSRPYKAAAAQLPETLETIMLLGLLGTVSLGIFFV LMRNKGIGKMGFGMVTLGASAWLMWLSEIEPARIACVLIVVFLLLVVLIPEPEKQRSP QDNQMAIIIMVAVGLLGLITANELGWLERTKSDLSHLMGRREEGATIGFSMDIDLRPA SAWAIYAALTTFITPAVQHAVTTSYNNYSLMAMATQAGVLFGMGKGMPFYAWDFGVPL LMIGCYSQLTPLTLIVAIILLVAHYMYLIPGLQAAAARAAQKRTAAGIMKNPVVDGIV VTDIDTMTIDPQVEKKMGQVLLIAVAVSSAILSRTAWGWGEAGALITAATSTLWEGSP NKYWNSSTATSLCNIFRGSYLAGASLIYTVTRNAGLVKRRGGGTGETLGEKWKARLNQ MSALEFYSYKKSGITEVCREEARRALKDGVATGGHAVSRGSAKLRWLVERGYLQPYGK VIDLGCGRGGWSYYAATIRKVQEVKGYTKGGPGHEEPVLVQSYGWNIVRLKSGVDVFH MAAEPCDTLLCDIGESSSSPEVEEARTLRVLSMVGDWLEKRPGAFCIKVLCPYTSTMM ETLERLQRRYGGGLVRVPLSRNSTHEMYWVSGAKSNTIKSVSTTSQLLLGRMDGPRRP VKYEEDVNLGSGTRAVVSCAEAPNMKIIGNRIERIRSEHAETWFFDENHPYRTWAYHG SYEAPTQGSASSLINGVVRLLSKPWDVVTGVTGIAMTDTTPYGQQRVFKEKVDTRVPD PQEGTRQVMSMVSSWLWKELGKHKRPRVCTKEEFINKVRSNAALGAIFEEEKEWKTAV EAVNDPRFWALVDKEREHHLRGECQSCVYNMMGKREKKQGEFGKAKGSRAIWYMWLGA RFLEFEALGFLNEDHWMGRENSGGGVEGLGLQRLGYVLEEMSRIPGGRMYADDTAGWD TRISRFDLENEALITNQMEKGHRALALAIIKYTYQNKVVKVLRPAEKGKTVMDIISRQ DQRGSGQVVTYALNTFTNLVVQLIRNMEAEEVLEMQDLWLLRRSEKVTNWLQSNGWDR LKRMAVSGDDCVVKPIDDRFAHALRFLNDMGKVRKDTQEWKPSTGWDNWEEVPFCSHH FNKLHLKDGRSIVVPCRHQDELIGRARVSPGAGWSIRETACLAKSYAQMWQLLYFHRR DLRLMANAICSSVPVDWVPTGRTTWSIHGKGEWMTTEDMLVVWNRVWIEENDHMEDKT PVTKWTDIPYLGKREDLWCGSLIGHRPRTTWAENIKNTVNMVRRIIGDEEKYMDYLST QVRYLGEEGSTPGVL" mat_peptide 101..466 /product="anchored capsid protein C" mat_peptide 101..412 /product="capsid protein C" mat_peptide 467..970 /product="membrane glycoprotein precursor M" mat_peptide 467..745 /product="protein pr" mat_peptide 746..970 /product="membrane glycoprotein M" mat_peptide 971..2482 /product="envelope protein E" mat_peptide 2483..3538 /product="nonstructural protein NS1" mat_peptide 3539..4216 /product="nonstructural protein NS2A" mat_peptide 4217..4606 /product="nonstructural protein NS2B" mat_peptide 4607..6457 /product="nonstructural protein NS3" mat_peptide 6458..6838 /product="nonstructural protein NS4A" mat_peptide 6839..6907 /product="protein 2K" mat_peptide 6908..7660 /product="nonstructural protein NS4B" mat_peptide 7661..10369 /product="RNA-dependent RNA polymerase NS5" 3'UTR 10373..10795 ORIGIN 1 gatctgtgtg aatcagactg cgacagttcg agtttgaagc gaaagctagc aacagtatca 61 acaggtttta ttttggattt ggaaacgaga gtttctggtc atgaaaaacc caaaaaagaa 121 atccggagga ttccggattg tcaatatgct aaaacgcgga gtagcccgtg tgagcccctt 181 tgggggcttg aagaggctgc cagccggact tctgctgggt catgggccca tcaggatggt 241 cttggcgatt ctagcctttt tgagattcac ggcaatcaag ccatcactgg gtctcatcaa 301 tagatggggt tcagtgggga aaaaagaggc tatggaaata ataaagaagt tcaagaaaga 361 tctggctgcc atgctgagaa taatcaatgc taggaaggag aagaagagac gaggcgcaga 421 tactagtgtc ggaattgttg gcctcctgct gaccacagct atggcagcgg aggtcactag 481 acgtgggagt gcatactaca tgtacttgga cagaaacgat gctggggagg ccatatcttt 541 tccaaccaca ttggggatga ataagtgtta tatacagatc atggatcttg gacacatgtg 601 tgatgccacc atgagctatg aatgccctat gctggatgag ggggtggaac cagatgacgt 661 cgattgttgg tgcaacacga cgtcaacttg ggttgtgtac ggaacctgcc atcacaaaaa 721 aggtgaagca cggagatcta gaagagctgt gacgctcccc tcccattcca ctaggaagct 781 gcaaacgcgg tcgcaaacct ggttggaatc gagagaatac acaaagcact tgattagagt 841 cgaaaattgg atattcagga accctggctt cgcgttagca gcagctgcca tcgcttggct 901 tttgggaagc tcaacgagcc aaaaagtcat atacttggtc atgatactgc tgattgcccc 961 ggcatacagc atcaggtgca taggagtcag caatagggac tttgtggaag gtatgtcagg 1021 tgggacttgg gttgatgttg tcttggaaca tggaggttgt gtcaccgtaa tggcacagga 1081 taaaccgact gtcgacatag agctggttac aacaacagtc agcaacatgg cggaggtaag 1141 atcctactgc tatgaggcat caatatcaga catggcttcg gacagccgct gcccaacaca 1201 aggtgaagcc taccttgaca agcaatcaga cactcaatat gtctgcaaaa gaacgttagt 1261 ggacagaggc tggggaaatg gatgtggact ttttggcaaa gggagcctgg tgacatgcgc 1321 taagtttgca tgctccaaga aaatgaccgg gaagagcatc cagccagaga atctggagta 1381 ccggataatg ctgtcagttc atggctccca gcacagtggg atgatcgtta atgacacagg 1441 acatgaaact gatgagaata gagcgaaggt tgagataacg cccaattcac caagagccga 1501 agccaccctg gggggttttg gaagcctagg acttgattgt gaaccgagga caggccttga 1561 cttttcagat ttgtattact tgactatgaa taacaagcac tggttggttc acaaggagtg 1621 gttccacgac attccattgc cttggcacgc tggggcagac accggaactc cacactggaa 1681 caacaaagaa gcactggtag agttcaagga cgcacatgcc aaaaggcaaa ctgtcgtggt 1741 tctagggagt caagaaggag cagttcacac ggcccttgct ggagctctgg aggctgagat 1801 ggatggtgca aagggaaggc tgtcctctgg ccacttgaaa tgtcgcctga aaatggataa 1861 acttagattg aagggcgtgt catactcctt gtgtaccgca gcgttcacat tcaccaagat 1921 cccggctgaa acactgcacg ggacagtcac agtggaggta cagtacgcag ggacagatgg 1981 accttgcaag gttccagctc agatggcggt ggacatgcaa actctgaccc cagttgggag 2041 gttgataacc gctaaccccg taatcactga aagcactgag aactctaaga tgatgctgga 2101 acttgatcca ccatttgggg actcttacat tgtcatagga gtcggggaga agaagatcac 2161 ccaccactgg cacaggagtg gcagcaccat tggaaaagca tttgaagcca ctgtgagagg 2221 tgccaagaga atggcagtct tgggagacac agcctgggac tttggatcag ttggaggcgc 2281 tctcaactca ttgggcaagg gcatccatca aatttttgga gcagctttca aatcattgtt 2341 tggaggaatg tcctggttct cacaaattct cattggaacg ttgctgatgt ggttgggcct 2401 gaacacaaag aatggatcta tttcccttat gtgcttggcc ttagggggag tgttgatctt 2461 cttatccaca gccgtctctg ctgatgtggg gtgctcggtg gacttctcaa agaaggagac 2521 gagatgcggt acaggggtgt tcgtctataa cgacgttgaa gcctggaggg acaggtacaa 2581 gtaccatcct gactcccccc gtagattggc agcagcagtc aagcaagcct gggaagatgg 2641 tatctgcggg atctcctctg tttcaagaat ggaaaacatc atgtggagat cagtagaagg 2701 ggagctcaac gcaatcctgg aagagaatgg agttcaactg acggtcgttg tgggatcggt 2761 aaaaaacccc atgtggagag gtccacagag attgcccgtg cctgtgaacg agctgcccca 2821 cggctggaag gcttggggga aatcgtactt cgtcagagca gcaaagacaa ataacagctt 2881 tgtcgtggat ggtgacacac tgaaggaatg cccactcaaa catagagcat ggaacagctt 2941 tcttgtggag gatcatgggt tcggggtatt tcacactagt gtctggctca aggttagaga 3001 agattattca ttagagtgtg atccagccgt tattggaaca gctgttaagg gaaaggaggc 3061 tgtacacagt gatctaggct actggattga gagtgagaag aatgacacat ggaggctgaa 3121 gagggcccat ctgatcgaga tgaaaacatg tgaatggcca aagtcccaca cattgtggac 3181 agatggaata gaagagagtg atctgatcat acccaagtct ttagctgggc cactcagcca 3241 tcacaatacc agagagggct acaggaccca aatgaaaggg ccatggcaca gtgaagagct 3301 tgaaattcgg tttgaggaat gcccaggcac taaggtccac gtggaggaaa catgtggaac 3361 aagaggacca tctctgagat caaccactgc aagcggaagg gtgatcgagg aatggtgctg 3421 cagggagtgc acaatgcccc cactgtcgtt ccgggctaaa gatggctgtt ggtatggaat 3481 ggagataagg cccaggaaag aaccagaaag caacttagta aggtcaatgg tgactgcagg 3541 atcaactgat cacatggatc acttctccct tggagtgctt gtgattctgc tcatggtgca 3601 ggaagggctg aagaagagaa tgaccacaaa gatcatcata agcacatcaa tggcagtgct 3661 ggtagctatg atcctgggag gattttcaat gagtgacctg gctaagcttg caattttgat 3721 gggtgccacc ttcgcggaaa tgaacactgg aggagatgta gctcatctgg cgctgatagc 3781 ggcattcaaa gtcagaccag cgttgctggt atctttcatc ttcagagcta attggacacc 3841 ccgtgaaagc atgctgctgg ccttggcctc gtgtcttttg caaactgcga tctccgcctt 3901 ggaaggcgac ctgatggttc tcatcaatgg ttttgctttg gcctggttgg caatacgagc 3961 gatggttgtt ccacgcactg ataacatcac cttggcaatc ctggctgctc tgacaccact 4021 ggcccggggc acactgcttg tggcgtggag agcaggcctt gctacttgcg gggggtttat 4081 gctcctctct ctgaagggaa aaggcagtgt gaagaagaac ttaccatttg tcatggccct 4141 gggactaacc gctgtgaggc tggtcgaccc catcaacgtg gtgggactgc tgttgctcac 4201 aaggagtggg aagcggagct ggccccctag cgaagtactc acagctgttg gcctgatatg 4261 cgcattggct ggagggttcg ccaaggcaga tatagagatg gctgggccca tagccgcggt 4321 cggtctgcta attgtcagtt acgtggtctc aggaaagagt gtggacatgt acattgaaag 4381 agcaggtgac atcacatggg aaaaagatgc ggaagtcact ggaaacagtc cccggctcga 4441 tgtggcgcta gatgagagtg gtgatttctc cctggtggag gatgacggtc cccccatgag 4501 agagatcata ctcaaggtgg tcctgatgac catctgtggc atgaacccaa tagccatacc 4561 ttttgcagct ggagcgtggt acgtatacgt gaagactgga aaaaggagtg gtgctctatg 4621 ggatgtgcct gctcccaagg aagtaaaaaa gggggagacc acagatggag tgtacagagt 4681 aatgactcgt agactgctgg gttcaacaca agttggagtg ggagttatgc aagagggggt 4741 ctttcacact atgtggcacg tcacaaaagg atccgcactg agaagcggtg aagggagact 4801 tgatccatac tggggagatg tcaagcagga tctggtgtca tactgtggtc catggaagct 4861 agatgccgcc tgggacgggc acagcgaggt gcagctcttg gccgtgcccc ccggagagag 4921 agcgaggaac atccagactc tgcccggaat atttaagaca aaggatgggg acattggagc 4981 ggttgcgctg gattacccag caggaacttc aggatctcca atcctagaca agtgtgggag 5041 agtgatagga ctttatggca atggggtcgt gatcaaaaat gggagttatg ttagtgccat 5101 cacccaaggg aggagggagg aagagactcc tgttgagtgc ttcgagcctt cgatgctgaa 5161 gaagaagcag ctaactgtct tagacttgca tcctggagct gggaaaacca ggagagttct 5221 tcctgaaata gtccgtgaag ccataaaaac aagactccgt actgtgatct tagctccaac 5281 cagggttgtc gctgctgaaa tggaggaggc ccttagaggg cttccagtgc gttatatgac 5341 aacagcagtc aatgtcaccc actctggaac agaaatcgtc gacttaatgt gccatgccac 5401 cttcacttca cgtctactac agccaatcag agtccccaac tataatctgt atattatgga 5461 tgaggcccac ttcacagatc cctcaagtat agcagcaaga ggatacattt caacaagggt 5521 tgagatgggc gaggcggctg ccatcttcat gaccgccacg ccaccaggaa cccgtgacgc 5581 atttccggac tccaactcac caattatgga caccgaagtg gaagtcccag agagagcctg 5641 gagctcaggc tttgattggg tgacggatca ttctggaaaa acagtttggt ttgttccaag 5701 cgtgaggaac ggcaatgaga tcgcagcttg tctgacaaag gctggaaaac gggtcataca 5761 gctcagcaga aagacttttg agacagagtt ccagaaaaca aaacatcaag agtgggactt 5821 tgtcgtgaca actgacattt cagagatggg cgccaacttt aaagctgacc gtgtcataga 5881 ttccaggaga tgcctaaagc cggtcatact tgatggcgag agagtcattc tggctggacc 5941 catgcctgtc acacatgcca gcgctgccca gaggaggggg cgcataggca ggaatcccaa 6001 caaacctgga gatgagtatc tgtatggagg tgggtgcgca gagactgacg aagaccatgc 6061 acactggctt gaagcaagaa tgctccttga caatatttac ctccaagatg gcctcatagc 6121 ctcgctctat cgacctgagg ccgacaaagt agcagccatt gagggagagt tcaagcttag 6181 gacggagcaa aggaagacct ttgtggaact catgagaaga ggagatcttc ctgtttggct 6241 ggcctatcag gttgcatctg ccggaataac ctacacagat agaagatggt gctttgatgg 6301 cacgaccaac aacaccataa tggaagacag tgtgccggca gaggtgtgga ccagacacgg 6361 agagaaaaga gtgctcaaac cgaggtggat ggacgccaga gtttgttcag atcatgcggc 6421 cctgaagtca ttcaaggagt ttgccgctgg gaaaagagga gcggcttttg gagtgatgga 6481 agccctggga acactgccag gacacatgac agagagattc caggaagcca ttgacaacct 6541 cgctgtgctc atgcgggcag agactggaag caggccttac aaagccgcgg cggcccaatt 6601 gccggagacc ctagagacca ttatgctttt ggggttgttg ggaacagtct cgctgggaat 6661 ctttttcgtc ttgatgagga acaagggcat agggaagatg ggctttggaa tggtgactct 6721 tggggccagc gcatggctca tgtggctctc ggaaattgag ccagccagaa ttgcatgtgt 6781 cctcattgtt gtgttcctat tgctggtggt gctcatacct gagccagaaa agcaaagatc 6841 tccccaggac aaccaaatgg caatcatcat catggtagca gtaggtcttc tgggcttgat 6901 taccgccaat gaactcggat ggttggagag aacaaagagt gacctaagcc atctaatggg 6961 aaggagagag gagggggcaa ccataggatt ctcaatggac attgacctgc ggccagcctc 7021 agcttgggcc atctatgctg ccttgacaac tttcattacc ccagccgtcc aacatgcagt 7081 gaccacttca tacaacaact actccttaat ggcgatggcc acgcaagctg gagtgttgtt 7141 tggtatgggc aaagggatgc cattctacgc atgggacttt ggagtcccgc tgctaatgat 7201 aggttgctac tcacaattaa cacccctgac cctaatagtg gccatcattt tgctcgtggc 7261 gcactacatg tacttgatcc cagggctgca ggcagcagct gcgcgtgctg cccagaagag 7321 aacggcagct ggcatcatga agaaccctgt tgtggatgga atagtggtga ctgacattga 7381 cacaatgaca attgaccccc aagtggagaa aaagatggga caggtgctac tcatagcagt 7441 agccgtctcc agcgccatac tgtcgcggac cgcctggggg tggggggagg ctggggccct 7501 gatcacagcc gcaacttcca ctttgtggga aggctctccg aacaagtact ggaactcctc 7561 tacagccact tcactgtgta acatttttag gggaagttac ttggctggag cttctctaat 7621 ctacacagta acaagaaacg ctggcttggt caagagacgt gggggtggaa caggagagac 7681 cctgggagag aaatggaagg cccgcttgaa ccagatgtcg gccctggagt tctactccta 7741 caaaaagtca ggcatcaccg aggtgtgcag agaagaggcc cgccgcgccc tcaaggacgg 7801 tgtggcaacg ggaggccatg ctgtgtcccg aggaagtgca aagctgagat ggttggtgga 7861 gcggggatac ctgcagccct acggaaaggt cattgatctt ggatgtggca gagggggctg 7921 gagttactac gccgccacca tccgcaaagt tcaagaagtg aaaggataca caaaaggagg 7981 ccctggtcat gaagaacccg tgttggtgca aagctatggg tggaacatag tccgtcttaa 8041 gagtggggtg gacgtctttc atatggcggc tgagccgtgt gacacgttgc tgtgtgacat 8101 aggtgagtca tcatctagtc ctgaagtgga agaagcacgg acgctcagag tcctctccat 8161 ggtgggggat tggcttgaaa aaagaccagg agccttttgt ataaaagtgt tgtgcccata 8221 caccagcact atgatggaaa ccctggagcg actgcagcgt aggtatgggg gaggactggt 8281 cagagtgcca ctctcccgca actctacaca tgagatgtac tgggtctctg gagcgaaaag 8341 caacaccata aaaagtgtgt ccaccacgag ccagctcctc ttggggcgca tggacgggcc 8401 taggaggcca gtgaaatatg aggaggatgt gaatctcggc tctggcacgc gggctgtggt 8461 aagctgcgct gaagctccca acatgaagat cattggtaac cgcattgaaa ggatccgcag 8521 tgagcacgcg gaaacgtggt tctttgacga gaaccaccca tataggacat gggcttacca 8581 tggaagctat gaggccccca cacaagggtc agcgtcctct ctaataaacg gggttgtcag 8641 gctcctgtca aaaccctggg atgtggtgac tggagtcaca ggaatagcca tgaccgacac 8701 cacaccgtat ggtcagcaaa gagttttcaa ggaaaaagtg gacactaggg tgccagaccc 8761 ccaagaaggc actcgtcagg ttatgagcat ggtctcttcc tggttgtgga aagagctagg 8821 caaacacaaa cggccacgag tctgtaccaa agaagagttc atcaacaagg ttcgcagcaa 8881 tgcagcatta ggggcaatat ttgaagagga aaaagagtgg aagactgcag tggaagctgt 8941 gaacgatcca aggttctggg ctctagtgga caaggaaaga gagcaccacc tgagaggaga 9001 gtgccagagt tgtgtgtaca acatgatggg aaaaagagaa aagaaacaag gggaatttgg 9061 aaaggccaag ggcagccgcg ccatctggta tatgtggcta ggggctagat ttctagagtt 9121 cgaagccctt ggattcttga acgaggatca ctggatgggg agagagaact caggaggtgg 9181 tgttgaaggg ctgggattac aaagactcgg atatgtccta gaagagatga gtcgcatacc 9241 aggaggaagg atgtatgcag atgacactgc tggctgggac acccgcatca gcaggtttga 9301 tctggagaat gaagctctaa tcaccaacca aatggagaaa gggcacaggg ccttggcatt 9361 ggccataatc aagtacacat accaaaacaa agtggtaaag gtccttagac cagctgaaaa 9421 agggaaaaca gttatggaca ttatttcgag acaagaccaa agggggagcg gacaagttgt 9481 cacttacgct cttaacacat ttaccaacct agtggtgcaa ctcattcgga atatggaggc 9541 tgaggaagtt ctagagatgc aagacttgtg gctgctgcgg aggtcagaga aagtgaccaa 9601 ctggttgcag agcaacggat gggataggct caaacgaatg gcagtcagtg gagatgattg 9661 cgttgtgaag ccaattgatg acaggtttgc acatgccctc aggttcttga atgatatggg 9721 aaaagttagg aaggacacac aagagtggaa accctcaact ggatgggaca actgggaaga 9781 agttccgttt tgctcccacc acttcaacaa gctccatctc aaggacggga ggtccattgt 9841 ggttccctgc cgccaccaag atgaactgat tggccgggcc cgcgtctctc caggggcggg 9901 atggagcatc cgggagactg cttgcctagc aaaatcatat gcgcaaatgt ggcagctcct 9961 ttatttccat agaagggacc tccgactgat ggccaatgcc atttgttcat ctgtgccagt 10021 tgactgggtt ccaactggga gaactacctg gtcaatccat ggaaagggag aatggatgac 10081 cactgaagac atgcttgtgg tgtggaacag agtgtggatt gaggagaacg accacatgga 10141 agacaagacc ccagttacga aatggacaga cattccctat ttgggaaaaa gggaagactt 10201 gtggtgtgga tctctcatag ggcacagacc gcgcaccacc tgggctgaga acattaaaaa 10261 cacagtcaac atggtgcgca ggatcatagg tgatgaagaa aagtacatgg actacctatc 10321 cacccaagtt cgctacttgg gtgaagaagg gtctacacct ggagtgctgt aagcaccaat 10381 cttaatgttg tcaggcctgc tagtcagcca cagcttgggg aaagctgtgc agcctgtgac 10441 ccccccagga gaagctggga aaccaagcct atagtcaggc cgagaacgcc atggcacgga 10501 agaagccatg ctgcctgtga gcccctcaga ggacactgag tcaaaaaacc ccacgcgctt 10561 ggaggcgcag gatgggaaaa gaaggtggcg accttcccca cccttcaatc tggggcctga 10621 actggagatc agctgtggat ctccagaaga gggactagtg gttagaggag accccccgga 10681 aaacgcaaaa cagcatattg acgctgggaa agaccagaga ctccatgagt ttccaccacg 10741 ctggccgcca ggcacagatc gccgaatagc ggcggccggt gtggggaaat ccatg Link to comment Share on other sites More sharing options...
niman Posted March 24, 2016 Author Report Share Posted March 24, 2016 Sequences producing significant alignments:Select:AllNone Selected:0AlignmentsDownloadGenBankGraphicsDistance tree of resultsShow/hide columns of the table presenting sequences producing significant alignmentsSequences producing significant alignments:Select for downloading or viewing reportsDescriptionMax scoreTotal scoreQuery coverE valueIdentAccessionSelect seq gb|KU926309.1|Zika virus isolate Rio-U1, complete genome1852518525100%0.0100%KU926309.1Select seq gb|KU509998.1|Zika virus strain Haiti/1225/2014, complete genome1840818408100%0.099%KU509998.1Select seq gb|KJ776791.1|Zika virus strain H/PF/2013 polyprotein gene, complete cds1840218402100%0.099%KJ776791.1Select seq gb|KU707826.1|Zika virus isolate SSABR1, complete genome1839318393100%0.099%KU707826.1Select seq gb|KU365779.1|Zika virus strain BeH819966 polyprotein gene, complete cds1839318393100%0.099%KU365779.1Select seq gb|KU321639.1|Zika virus strain ZikaSPH2015, complete genome1839318393100%0.099%KU321639.1Select seq gb|KU729218.1|Zika virus isolate BeH828305 polyprotein gene, complete cds1838418384100%0.099%KU729218.1Select seq gb|KU501217.1|Zika virus strain 8375 polyprotein gene, complete cds1838118381100%0.099%KU501217.1Select seq gb|KU365780.1|Zika virus strain BeH815744 polyprotein gene, complete cds1838118381100%0.099%KU365780.1Select seq gb|KU501216.1|Zika virus strain 103344 polyprotein gene, complete cds1837518375100%0.099%KU501216.1Select seq gb|KU365777.1|Zika virus strain BeH818995 polyprotein gene, complete cds1837518375100%0.099%KU365777.1Select seq gb|KU729217.2|Zika virus isolate BeH823339 polyprotein gene, complete cds1836618366100%0.099%KU729217.2Select seq gb|KU647676.1|Zika virus strain MRS_OPY_Martinique_PaRi_2015 polyprotein gene, complete cds1836618366100%0.099%KU647676.1Select seq gb|KU365778.1|Zika virus strain BeH819015 polyprotein gene, complete cds1836318363100%0.099%KU365778.1Select seq gb|KU312312.1|Zika virus isolate Z1106033 polyprotein gene, complete cds1836318363100%0.099%KU312312.1Select seq gb|KU497555.1|Zika virus isolate Brazil-ZKV2015, complete genome183591835999%0.099%KU497555.1Select seq gb|KU527068.1|Zika virus strain Natal RGN, complete genome1835718357100%0.099%KU527068.1Select seq gb|KU820897.1|Zika virus isolate FLR polyprotein gene, complete cds1835418354100%0.099%KU820897.1Select seq gb|KU501215.1|Zika virus strain PRVABC59, complete genome1835418354100%0.099%KU501215.1Select seq gb|KU922960.1|Zika virus isolate MEX/InDRE/Sm/2016, complete genome1834818348100%0.099%KU922960.1Select seq gb|KU926310.1|Zika virus isolate Rio-S1, complete genome1834518345100%0.099%KU926310.1Select seq gb|KU922923.1|Zika virus isolate MEX/InDRE/Lm/2016, complete genome1834518345100%0.099%KU922923.1Select seq gb|KU853013.1|Zika virus isolate Dominican Republic/2016/PD2, complete genome1834518345100%0.099%KU853013.1Select seq gb|KU853012.1|Zika virus isolate Dominican Republic/2016/PD1, complete genome1834318343100%0.099%KU853012.1Select seq gb|KU820898.1|Zika virus isolate GZ01 polyprotein gene, complete cds1833618336100%0.099%KU820898.1Select seq gb|KU740184.2|Zika virus isolate GD01 polyprotein gene, complete cds1832718327100%0.099%KU740184.2Select seq gb|KU761564.1|Zika virus isolate GDZ16001 polyprotein gene, complete cds1832718327100%0.099%KU761564.1Select seq gb|KU820899.2|Zika virus isolate ZJ03, complete genome1830018300100%0.099%KU820899.2Select seq gb|KU866423.1|Zika virus isolate Zika virus/SZ01/2016 polyprotein gene, complete cds1819118191100%0.099%KU866423.1Select seq gb|KU744693.1|Zika virus isolate VE_Ganxian, complete genome1816818168100%0.099%KU744693.1Select seq gb|KU681081.3|Zika virus isolate Zika virus/H.sapiens-tc/THA/2014/SV0127- 14, complete genome1806018060100%0.099%KU681081.3Select seq gb|JN860885.1|Zika virus isolate FSS13025 polyprotein gene, partial cds177531775399%0.098%JN860885.1Select seq gb|KF993678.1|Zika virus strain PLCal_ZV from Canada polyprotein gene, partial cds177061770698%0.099%KF993678.1Select seq gb|EU545988.1|Zika virus polyprotein gene, complete cds1760317603100%0.098%EU545988.1Select seq gb|KU681082.3|Zika virus isolate Zika virus/H.sapiens-tc/PHL/2012/CPC-0740, complete genome1744717447100%0.098%KU681082.3Select seq gb|HQ234499.1|Zika virus isolate P6-740 polyprotein gene, partial cds164201642099%0.095%HQ234499.1Select seq gb|KF383115.1|Zika virus strain ArB1362 polyprotein gene, complete cds1329713297100%0.089%KF383115.1Select seq gb|KU720415.1|Zika virus strain MR 766 polyprotein gene, complete cds1329013290100%0.089%KU720415.1Select seq gb|KF268948.1|Zika virus isolate ARB13565 polyprotein gene, complete cds1328413284100%0.089%KF268948.1Select seq gb|HQ234498.1|Zika virus isolate MR_766 polyprotein gene, partial cds132841328499%0.089%HQ234498.1Select seq gb|KF268950.1|Zika virus isolate ARB7701 polyprotein gene, complete cds1327713277100%0.089%KF268950.1Select seq gb|KF268949.1|Zika virus isolate ARB15076 polyprotein gene, complete cds1327513275100%0.089%KF268949.1Select seq gb|DQ859059.1|Zika virus strain MR 766 polyprotein gene, complete cds1327513275100%0.089%DQ859059.1Select seq dbj|LC002520.1|Zika virus genomic RNA, complete genome, strain: MR766-NIID1326813268100%0.089%LC002520.1Select seq gb|KF383119.1|Zika virus strain ArD158084 polyprotein gene, complete cds1326313263100%0.089%KF383119.1Select seq gb|KF383116.1|Zika virus strain ArD7117 polyprotein gene, complete cds1323013230100%0.089%KF383116.1Select seq gb|HQ234501.1|Zika virus isolate ArD_41519 polyprotein gene, partial cds132141321499%0.089%HQ234501.1Select seq gb|AY632535.2|Zika virus strain MR 766, complete genome1320913209100%0.089%AY632535.2Select seq gb|KF383117.1|Zika virus strain ArD128000 polyprotein gene, complete cds1316013160100%0.088%KF383117.1Select seq gb|HQ234500.1|Zika virus isolate IbH_30656 polyprotein gene, partial cds131441314499%0.088%HQ234500.1Select seq gb|KF383118.1|Zika virus strain ArD157995 polyprotein gene, complete cds1294013008100%0.088%KF383118.1Select seq gb|KF383121.1|Zika virus strain ArD158095 polyprotein gene, partial cds128611286197%0.089%KF383121.1Select seq gb|KF383120.1|Zika virus strain ArD142623 nonfunctional polyprotein gene, partial sequence108621086297%0.084%KF383120.1Select seq gb|KU312314.1|Zika virus isolate Z1106031 polyprotein gene, partial cds4971497127%0.099%KU312314.1Select seq gb|KU312313.1|Zika virus isolate Z1106032 polyprotein gene, partial cds4944494427%0.099%KU312313.1Select seq gb|KU646828.1|Zika virus isolate Si322 polyprotein gene, partial cds4655465525%0.099%KU646828.1Select seq gb|KU646827.1|Zika virus isolate Si323 polyprotein gene, partial cds4646464625%0.099%KU646827.1Select seq gb|KU312315.1|Zika virus isolate Z1106027 polyprotein gene, partial cds3434343418%0.099%KU312315.1Select seq gb|KU740199.1|Zika virus isolate VE_Ganxian2016 polyprotein gene, partial cds3211321117%0.099%KU740199.1Select seq gb|DQ859064.1|Spondweni virus strain SM-6 V-1 polyprotein gene, complete cds2852418495%0.071%DQ859064.1Select seq gb|KJ634273.1|Zika virus strain CK-ISL 2014 E protein (E) gene, partial cds2691269114%0.099%KJ634273.1Select seq gb|KU686218.1|Zika virus isolate MEX/InDRE/14/2015 polyprotein gene, partial cds2048204811%0.099%KU686218.1Select seq gb|KU179098.1|Zika virus isolate JMB-185 nonstructural protein 5 gene, partial cds2017201711%0.099%KU179098.1Select seq gb|KM078936.1|Zika virus strain CHI1410214 NS5 protein gene, partial cds174617469%0.099%KM078936.1Select seq gb|KM078961.1|Zika virus strain CHI2612114 NS5 protein gene, partial cds174517459%0.099%KM078961.1Select seq gb|KM078930.1|Zika virus strain CHI2283714 NS5 protein gene, partial cds174317439%0.099%KM078930.1Select seq gb|KM078971.1|Zika virus strain CHI2613014 NS5 protein gene, partial cds173917399%0.099%KM078971.1Select seq gb|KM078970.1|Zika virus strain CHI2490414 NS5 protein gene, partial cds173917399%0.099%KM078970.1Select seq gb|KM078933.1|Zika virus strain CHI1058514 NS5 protein gene, partial cds173917399%0.099%KM078933.1Select seq gb|KM078929.1|Zika virus strain CHI1805214 NS5 protein gene, partial cds173717379%0.099%KM078929.1Select seq gb|KJ873160.1|Zika virus isolate NC14-03042014-3481 nonstructural protein 5 gene, partial cds159715978%0.099%KJ873160.1Select seq gb|KJ873161.1|Zika virus isolate NC14-02042014-3220 nonstructural protein 5 gene, partial cds141614167%0.099%KJ873161.1Select seq gb|KM851039.1|Zika virus strain SV0127/14 nonstructural protein 5 gene, partial cds137913797%0.099%KM851039.1Select seq gb|KU556802.1|Zika virus isolate MEX/InDRE/14/2015 NS5 protein gene, partial cds134613467%0.099%KU556802.1Select seq gb|KM851038.1|Zika virus strain CPC-0740 nonstructural protein 5 gene, partial cds134213427%0.098%KM851038.1Select seq gb|AF013415.1|Zika virus strain MR-766 NS5 protein (NS5) gene, partial cds1301130110%0.088%AF013415.1Select seq gb|KU232300.1|Zika virus isolate 067ZV_PEBR15 NS5 protein gene, partial cds124012406%0.099%KU232300.1Select seq gb|KT200609.1|Zika virus isolate BR/949/15 NS5 gene, partial cds124012406%0.099%KT200609.1Select seq gb|KU232290.1|Zika virus isolate 036ZV_PEBR15 NS5 protein gene, partial cds123112316%0.099%KU232290.1Select seq gb|KU232297.1|Zika virus isolate 049ZV_PEBR15 NS5 protein gene, partial cds122912296%0.099%KU232297.1Select seq gb|KU232294.1|Zika virus isolate 061ZV_PEBR15 NS5 protein gene, partial cds122012206%0.099%KU232294.1Select seq gb|KU232292.1|Zika virus isolate 054ZV_PEBR15 NS5 protein gene, partial cds121812186%0.099%KU232292.1Select seq gb|KU232298.1|Zika virus isolate 050ZV_PEBR15 NS5 protein gene, partial cds121412146%0.099%KU232298.1Select seq gb|KU232296.1|Zika virus isolate 045ZV_PEBR15 NS5 protein gene, partial cds121112116%0.099%KU232296.1Select seq gb|KU232293.1|Zika virus isolate 057ZV_PEBR15 NS5 protein gene, partial cds121112116%0.099%KU232293.1Select seq gb|KU232295.1|Zika virus isolate 068ZV_PEBR15 NS5 protein gene, partial cds120512056%0.099%KU232295.1Select seq gb|KU232288.1|Zika virus isolate 001ZV_PEBR15 NS5 protein gene, partial cds119511956%0.099%KU232288.1Select seq gb|KU232289.1|Zika virus isolate 020ZV_PEBR15 NS5 protein gene, partial cds119111916%0.099%KU232289.1Select seq gb|KU232299.1|Zika virus isolate 015ZV_PEBR15 NS5 protein gene, partial cds118711876%0.099%KU232299.1Select seq gb|KU232291.1|Zika virus isolate 051ZV_PEBR15 NS5 protein gene, partial cds118611866%0.099%KU232291.1Select seq gb|KU758878.1|Zika virus polyprotein gene, partial cds113311336%0.099%KU758878.1Select seq gb|KF270886.1|Zika virus strain CCB-870 envelope glycoprotein gene, partial cds107210728%0.088%KF270886.1Select seq gb|KU867812.1|Zika virus isolate Jiangxi.CHN/01/2016 nonstructural protein 5 gene, partial cds100910095%0.099%KU867812.1 Link to comment Share on other sites More sharing options...
niman Posted March 24, 2016 Author Report Share Posted March 24, 2016 Sequence map updatehttps://www.google.com/maps/d/u/0/edit?mid=zv94AJqgUct4.kI8kcFySb4J0&hl=en Link to comment Share on other sites More sharing options...
niman Posted March 24, 2016 Author Report Share Posted March 24, 2016 Link to comment Share on other sites More sharing options...
niman Posted March 24, 2016 Author Report Share Posted March 24, 2016 S1 Table Clinical symptomsPatient1234Onset date01/11/1601/24/1601/22/1601/31/16Days after symptoms onset *3251Days after rash onset *<1**111Rash duration5 days6 days2 days2 daysRash typeMacularMacular and maculo-papularMaculo-papularMaculo-papularLow grade fever(duration)-+ (2 days)+ (4 days)-Headache--+-Retro-orbital pain--+-Photophobia--NI-Fatigue/ malaise-++-Myalgia-++-Arthralgia(region)+ (wrist and elbows)-+ (large and small joints)-Arthritis----Anorexia--+-Nausea/ vomiting--+-Diarrhea----Abdominal pain----Dysuria----Bleeding/ petechia----Dizziness/ light headedness----Pruritus+-++Paresthesias+---Conjunctivitis----Edema(local/site)+ (hands)---Lymphadenopathy(local/ site)----EnanthemNI-NI-Respiratory symptoms----Jaundice----Seizures----* Regarding the date of sample collection; **the collection date was in the first day of rash manifestation S2 TableClinical symptomsPatient56789Onset date01/26/1601/26/1601/31/1601/31/1601/28/16Days after sypmtons onset *23125Days after rash onset *2<1122Rash duration 20 days 4 days5 days6 days3 daysRash typeMacularMaculo-papularMaculo-papularMacular and maculo-papularMaculo-papularLow grade fever(duration)-+ (1 day)-+ (2 days)-Headache+--++Retro-orbital pain+--++Photophobia+---+Fatigue/ malaise++-+-Myalgia++--+Arthralgia(region)-+ (wrists, ankles, knees, hands)-+ (large and small joints)-Arthritis-----Anorexia++---Nausea/ vomiting+----Diarrhea+----Abdominal pain-+---Dysuria-----Bleeding/ petechia ----Dizziness/ light headedness+----Pruritus+++++Paresthesias++---Conjunctivitis++--+Edema+ (feet and hands) +(hands)-+-Lymphadenopathy(local/ site)+(Cervical and auricular)---+(cervical)Enanthem-----Respiratory symptoms +--+-Jaundice-----Seizures-----* Regarding the date of sample collection; **the collection date was in the first day of rash manifestation S3 Table Social-demographic dataPatient1234GenderfemalefemalemalefemaleAge36302442Gestational age (weeks)1833NA21Family members illness--+-Partner illness--NI-Repellent spray use++NI+Previous DENV infection+-NI-Domicile in Rio de Janeiro StateDuque de CaxiasNova IguaçuRio de JaneiroDuque de CaxiasNA – not applicable; NI- not informed S4 Table Social demographic dataPatient56789Gender femalemalefemalefemalefemaleAge3068202722Gestational age (weeks)NANA172120Family members illness-+---Partner illness-----Repellent spray use+-+++Previous DENV infection++-+-Domicile in Rio de Janeiro StateRio de JaneiroRio de JaneiroRio de JaneiroDuque de CaxiasRio de JaneiroNA – not applicable; NI- not informed Link to comment Share on other sites More sharing options...
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